[R] transition matrices

[Christos Hatzis]

I think what you are looking for is also called seriation or ordination,
i.e. find the "best" enumeration order of a set of objects.

Take a look at the following link for more information and on criteria for
defining "best"

http://www.lirmm.fr/~caraux/PermutMatrix/EN/Seriation.htm

The link is for a windows application (PermutMatrix) that can perform
seriation on distance matrices used in hierarchical clustering, but might be
useful in your context as well.

-Christos

Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830
www.nuverabio.com
 
  

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Richard Rowe
> Sent: Wednesday, April 04, 2007 2:35 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] transition matrices
> 
> I am working with transition matrices of sequences of animal 
> behaviours.  What I would like to do is parse the original 
> matrices, adjusting row/column order so that the matrix has 
> its main values in blocks surrounding the diagonal.  This 
> would cause behaviours involved in functional groupings (e.g. 
> grooming, resting, foraging etc) to appear as blocks.
> This can be done manually by applying subjective 'prior 
> knowledge' of sequences, however I would like to have an 
> algorithmic/objective method to generate at least a first cut ...
> Any suggestions or hints (even just thoughts) would be much 
> appreciated,
> 
> Richard Rowe
> 
> Dr Richard Rowe
> Zoology & Tropical Ecology
> School of Tropical Biology
> James Cook University
> Townsville 4811
> AUSTRALIA
> 
> ph +61 7 47 81 4851
> fax +61 7 47 25 1570
> JCU has CRICOS Provider Code 00117J
> 
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